The use of microorganisms to conduct modification of biomass for the production of bioenergy products or metabolites has been proposed in the art. Such process, ideally, would require two major types of activities: (i) a degradation activity, to transform biomass into fermentable sugars and (ii) a fermentation activity, to transform said sugars into bioenergy products or other valuable metabolites. So far, efforts have been directed mainly towards the identification of microorganisms having the ability to catalyze the fermentation step.
A monograph on the production of ethanol through fermentation with microorganisms was published under the title “Ethanol Fermentation Strains” by J. R. Hettenhaus, under the aegis of the United States Department of Energy and the National Renewable Energy Laboratory (Dec. 16, 1998). In this document, which summarizes the contributions made by participants in the study, it is pointed out that:                only microorganisms similar to Saccharomyces, Zymomonas and E. coli can be used in existing equipment;        in the short term, the increased fermentation of xylose and arabinose could be the main objective, it being specified however that it is of little interest to increase the converting efficacy of the other sugars of hexose or oligomer type;        over the longer term, gains could be achieved regarding higher operating temperatures and combining of the steps of enzyme production, saccharification and hydrolysis.        
Current industrial processes only allow the culture and growth of microorganisms for the fermentation and extraction of ethanol at temperatures in the region of 30° C., owing to the fragility of the industrial microorganisms (yeasts) used. They also entail major bioenergy costs to concentrate the ethanol after fermentation, since yeasts currently used for this fermentation cannot withstand ethanol concentrations above 100 g/l. Additionally, the fermentation of yeasts practically only uses C6 sugars, of glucose type.
The conversion of biomass using microorganisms has also been tested (Blumer-Schuette et al., 2008, Extremely thermophilic microorganisms for biomass conversion: status and prospects, Curr Opinion Biotechnol 19, pp. 210-217; Perez et al., 2002, Int Microbiol 5, pp 53-63). However, as reported in Mosier et al. (Bioresource Technology 96 (2005) 673-686), a pre-treatment of lignocellulosic biomass is required to alter the structure of cellulosic biomass to make cellulose more accessible to the enzymes that convert the carbohydrate polymers into fermentable sugars.
The industrial and efficient production of fermentable sugars (e.g., monomeric sugars) from raw (i.e., starch, lignocellulosic) biomass still remains a challenge.
Various approaches have been proposed to exploit biomass, such as thermochemical methods, acid hydrolysis or enzymatic hydrolysis. Sun H et al (Appl Biochem Biotechnol. 2010 February; 160(4):988-1003) discusses the use of enzymes for the degradation of starch. Polizeli M L et al, and Collin T et al (Appl Microbiol Biotechnol. 2005 June; 67(5):577-591; FEMS Microbiol Rev. 2005 January; 29(1):3-23) review the use of enzymes for the degradation of xylan. Wilson D B et al (Curr Opin Biotechnol. 2009 June; 20(3):295-299) discusses the use of enzymes for the degradation of cellulose for biofuel applications. In the case of lignin, only very few methods have been considered which imply the use of organo-solvents and incineration.